Sunday, December 14, 2014

Aside from the rhetorical work around the possible suspension of living processes (as presumably overthrowing a vitalistic notion that a lack of motion somehow means the organism is no longer alive), this observation from David Penny is interesting:

In reality, we already know that there is nothing in biology that is inconsistent with physics, chemistry and mathematics. In one of the most fundamental biological experiments in the twentieth century, Harold Morowitz and colleagues took cysts of the complex multicellular brine shrimp Artemia down to 2.2 degrees Kelvin (less than –270 °C), left them for six days, then slowly warmed them to room temperature, where they revived, grew and reproduced. At such low temperatures, information on energy levels, positions and velocities of electrons is lost; the only information left is about the chemicals and their relative positions. This tells us (as discussed in Penny D (2005) Biol Philos 20: in the press) that the composition and organization of chemicals is all that is required for a system to be alive. [emphases mine]

The composition and organization of the biochemical machinery in the cells is the embodiment of information. Information that is independent of the energy levels, positions, and velocities of electrons, much as would have been predicted by Polanyi's "Life's Irreducibility." Polanyi agreed that life was not inconsistent with physics and chemistry--but it wasn't explained by them. Aside from the insight of the experiment (as opposed to the lesson drawn by Penny), the reductionist fallacy is unhelpful:

The low-level information of particular particles turns out to be unnecessary for the organism to recover its machine-like thermodynamic process.
___________________________________________
Therefore, organization is sufficient for life.

Life can be suspended, therefore it is limited to a particular kind of organization (the kind that is presumably measurable). Reminds me of the reasoning that missed the early discovery of vitamin D. If a human being could be frozen in the same way, would that mean that there is nothing more to persons than their observable structure? Organization could be sufficient for the simplest examples of life. Or not. But the reasoning seems terribly flawed and overweening. Non-simulated "artificial life" has always involved already living cells.

Penny seems to be replacing physical reductionism with biochemical reductionism. It all reduces to structure. No need for physics envy here: My biochemistry is bigger than your physics. Ahem. Here's what you can do with your electrons.

The low-level information of electrons turns out to be so much noise, compared to the functional information stored in the organism's structure. I'm skeptical about much else beyond that significant observation, but then in this day and age any skepticism about orthodox precepts can make you a "denier."

It's interesting from the standpoint of this question: What sort of dissipative systems are as dependent (fundamentally) on the thermodynamic state (distribution of energy levels and particle momenta) as on the structural configuration?

Friday, December 12, 2014

In science's pecking order, evolutionary biology lurks somewhere near the bottom, far closer to phrenology than to physics. For evolutionary biology is a historical science, laden with history's inevitable imponderables. We evolutionary biologists cannot generate a Cretaceous Park to observe exactly what killed the dinosaurs; and, unlike "harder" scientists, we usually cannot resolve issues with a simple experiment, such as adding tube A to tube B and noting the color of the mixture.

But wait, hasn't the academic priesthood community averred loudly and proudly that doubting "evolution" (presuming the equivocal term includes the historical narrative) is like doubting gravity? (Look up discussions about whether or not evolution is "just a theory.") Eugenie Scott, former head of the Darwinist lobby think-tank NCSE, would say so.

How much of physics could you do without at least the Newtonian concept of gravity? There's a lot of experiment that can't be done without the Einsteinian conception of gravity. Yet Coyne was implying that as far as he knew in 2000, his field was largely irrelevant to experimental biology. Is the historical science of evolution central to biology in a very different way than gravity being central to physical theory?

Let's review Philip Skell's statement in "The Scientist":

"While the great majority of biologists would probably agree with Theodosius Dobzhansky's dictum that 'nothing in biology makes sense except in the light of evolution,' most can conduct their work quite happily without particular reference to evolutionary ideas," A.S. Wilkins, editor of the journal BioEssays, wrote in 2000. "Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superfluous one." I would tend to agree. Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming's discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No.
I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.

Re-read Coyne's "Vice" piece and Gould's famous Dr. Pangloss piece, and then think of what an "interesting narrative gloss" might mean.

Now, remember all those teachers in Texas who signed a petition because they were terrified that without a firm belief in the evolutionary narrative and the established power of selection, students would not be prepared for careers in biology. These teachers apparently were privy to something Jerry Coyne didn't know in 2000. I think Jerry has since doubted the superfluousness of evolution to medicine, but his supposed examples hinge on directed evolution and informational genetics. Ask yourself how directed evolution is different from artificial selection, the technology that inspired and long preceded Darwin. And Coyne wonders why biochemists and molecular biologists are turning on the evolutionary narrative?

I'm reminded of Jeffrey Shallit's comments (filed under "science stopper"?) that knowing that life is designed would turn out to be a completely uninteresting fact. (Just think about that statement on its own terms, and then think about how hard textbook writers have tried to ingrain the "central" idea that lifeforms are engineered by processes that are undirected, nonteleological, and purposeless.)

I can think of a way in which Shallit's statement could be construed as true. It could be true to the extent that modern biology already has a Designer. To some extent biology already treats lifeforms as engineered by a "watchmaker," if a "blind" one. But I can't rule out. Currently, it would seem the main reason that Jonathan Wells has had trouble getting visibility on his centrosome hypothesis, is that journals are afraid of giving any credibility to someone who doubts the central tenets of the priesthood profession.

Wednesday, December 10, 2014

Some people equate complexity with randomness/disorder because of algorithmic information is also called complexity.

Small probabilities tend to represent a highly select, unusual chain of contingencies. In the bean machine, the lefts vs. rights taken by the beans will have a more ordered structure at the tail ends. This low algorithmic information in tail-end result represents a path whose description has low algorithmic information.

How many things must go just right (or just wrong) to get the unusual result? It is highly contingent. Maybe specified contingency is a better phrase?

Monday, December 8, 2014

Has it not crossed Jeffrey Shallit's mind that Phillip Johnson is aware of those examples but doesn't find the case for the intermediate or transitional nature of those fossils very convincing? -- Jonathan M. on Shallit's claim that Phillip Johnson lied about the fossil record

Some notions of information are more closely tied to the Shannon notion of information (e.g. Thomas Schneider and Richard Dawkins) and tend not to wander much further. Much more closely related to some notion of meaning/function has been the Kolmogorov notion of information, also known as Kolmogorov complexity. Complexity and information tend to be closely related notions; both are related to probability, and probability has a combinatorial nature. The idea of mutual information is closely related to that of conditional probability. A complex thing generally needs more information to describe it (or information and time, but that will have to wait), while a much simpler thing generally required much less information. Highly improbable things tend to have many levels of contingencies, and convoluted histories/developments. Optimal codes match less probable events to more bits of information. An optimal code will tend to not only maximize the Shannon complexity of the messages but to also make the messages more compressed (maximizing K complexity per message length).

Jeffrey Shallit has become something of a public figure, not for math or computer science per se, but for being a "science defender" of the quixotic "anticreationist" variety. (Note: I have noticed Shallit also uses the term "anticreationist," though not in the ironic sense that I do.) He has made a name for himself ridiculing ideas and the people who promote them. He has complained in the past that 'specified complexity' would be better off called 'specified improbability.' His and Elsberry's long critique of the idea of 'complex specified information' scoffs at the difficulty in reducing CSI neatly to one of the two kinds of information . (Everything else is "creationist information.") Winston Ewert's notion of algorithmic specified complexity is very closely related to Dembski's notions of CSI and is itself a specie of randomness deficiency, combining notions of K-complexity and probability.

Something that is ubiquitous among complexity theorists and attempts to quantify 'biological information' is notably absent from Shallit's writings on the topic of complexity. It's what Jim Crutchfield calls 'humpology'. Most of the attempts over the last 20 years have tried to distinguish 'useful' information/complexity from both highly ordered and highly disordered configurations. Kolmogorov information considers highly disordered configurations to be provide more information, but most complexity theory tries to distinguish between useful information (what engineers typically mean by 'information': semantically "rich" information that carries some deep patterns) and the information maximized by total randomness. This fundamental concern in complexity theory doesn't seem to concern Shallit at all (which is odd given reasons that we'll get to).

Sunday, December 7, 2014

Has it not crossed Jeffrey Shallit's mind that Phillip Johnson is aware of those examples but doesn't find the case for the intermediate or transitional nature of those fossils very convincing? -- Jonathan M. on Shallit's claim that Phillip Johnson lied about the fossil record

Friday, December 5, 2014

From William Dembski's post about Jeffrey Shallit's nitpicks about information--the relationship between information and complexity is a lengthier subject--Seth Lloyd's non-exhaustive list of complexity measures:

Wednesday, December 3, 2014

Evolution is so much bigger (and more robust!) than Darwinism. Dawkins is a Darwinist but I'm not.

By Darwinism, you mean "Biology." "Darwinism" is a propaganda term invented by creationists.

It's possible that (2) is more likely to be espoused by educators and lobbyists than researchers. Richard Dawkins and Paul Gross probably exemplify (2). Off the top of my head, Larry Moran (Sandwalk), James Shapiro, Lynn Margulis, Rudolf Raff, and the Alternberg 16 scientists own to (1), although for some of them (1) might simply mean that there is more than one mechanism even though adaptation through selection is still the primary explanation for functional information (since selection depends far less on serendipity).

But the problem is exemplified in the recent Nature article in which biologists disagree about whether evolutionary biology is in great need of re-conception.

Depending on which biologist you ask, attacking selection is either attacking a straw man or attacking an unassailable, unquestionable foundation of biology. Point out this contradiction and the various factions will rally and point out that they all believe in evolution (cue "Book of Mormon" song "I Believe") and they all believe selection is important. Just in case the "non-existent" controversy "gives aid and comfort" to the Enemy.

And I say to the grownups, if you want to deny evolution and live in your world that's completely inconsistent with everything we observe in the universe, that's fine. But don't make your kids do it because we need them. We need scientifically literate voters and taxpayers for the future. We need engineers that can build stuff, solve problems.

Monday, December 1, 2014

I arrived at the university [Waterloo] to give my talk on 2013 November 28. I had never met Shallit, but I recognized him from the picture beside his blog. Just before starting my talk, I said “I'm surprised to see you here.”, to which he replied “I could use a laugh.”. I got no further than halfway down my first slide, having made one definition, when Shallit spoke up. He said that I had already gone wrong, and that there's no point in continuing. I replied that I am just starting to present the standard incomputability argument, and I haven't yet begun to talk about the problems with it. Shallit said that my version of the Halting Problem is nonstandard and faulty, and repeated that there's no point in continuing. I tried to continue, but Shallit would not allow me to. Other members of the audience joined the fight, all arguing against Shallit, saying that he should let me continue, and save his objections to the end. After that shaky start, having lost valuable time, I completed most of my talk and asked for questions. Shallit left.

On 2013 December 3, Shallit sent me an email saying that he had figured out where I went wrong, and how to set me straight.
- Eric Hehner, "The Shallit Affair"

Dr. Shallit was hoping to give new meaning to "Halting Problem," it seems.

General zip utilities tend to overlook real pattern as well. Is it possible that sophistication overlooks real structure because there aren't enough examples? Effective complexity is simply an approximation for what would be the real pattern in the data.

Friday, November 28, 2014

Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational’, they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle’.”
-- Wolfgang Pauli to Niels Bohr, 2/15/1955, letter 2015 in von Meyenn (2001), p.105

Thursday, November 27, 2014

We've been told by more than one of our colleagues that, even if Darwin was substantially wrong to claim that natural selection is the mechanism of evolution, nonetheless we shouldn't say so. Not, anyhow, in public. To do that is, however inadvertently, to align oneself with the Forces of Darkness, whose goal is to bring Science into disrepute. Well, we don't agree. We think the way to discomfort the Forces of Darkness is to follow the arguments wherever they may lead, spreading such light as one can in the course of doing so. What makes the Forces of Darkness dark is that they aren't willing to do that. What makes Science scientific is that it is.
-- Massimo Piattelli-Palmarini and Jerry Fodor, "What Darwin Got Wrong"

Monday, November 24, 2014

I was trying to locate somebody's article/post about the double message from academia about whether origins of life are properly part of evolution. I didn't find what I was looking for but I was amused at the first three hits on Google for Berkeley. The one marked "Misconception" is a short summary of the message to the negative. (This idea is often used as a counter-criticism of any criticism of the Urey-Miller experiments or of the state of 'origins of life' research.) Looking below at the other two and you see that at the same institution Evolution 101 doesn't start with cells like the Darwin cartoon above implies but it ends with cells and starts with soup. How we got from soup to cells is precisely the topic of 'origins of life'. 101 is usually the introductory material for a science, in this case evolutionary biology. In the other link, the subtitle to 'Origin of Life' is 'Understanding Evolution.' How do speculations about the "ultimate cold case" help a student understand a process that rather depends on cells already existing with their genetic code? It's not really Darwin's bag after all.

To understand the double-think about origins of life, I don't think you have to look any further than that the tenuity and the mutual contradiction of the hypotheses are much more obvious in origins of life than in evolutionary biology proper. The miraculousness and the void of sufficient material causes is also much more obvious. Hence the need for many to distance it from the rest of evolutionary biology for which the most general outlines have some consensus at least.

Thursday, October 16, 2014

Engineers know how important it is, and how much thought it takes, to create a storehouse of reusable components that can be assembled in various ways to do various things. The existence of a limited number of core processes that are essential for all forms of life, and used so artfully in so many different ways, demands a designer even more strongly than Paley’s watch. Life is not only complex, but it is optimally designed to make the broadest use of a limited number of proteins and processes. K&G want you to accept by faith, without proof, that all the biological core processes evolved by chance before the Precambrian era, and were able to assemble themselves into so many different configurations by luck because they had “weak linkage.” -- Do-While Jones

Wednesday, October 15, 2014

The number of biologists calling for change in how evolution is conceptualized is growing rapidly. Strong support comes from allied disciplines, particularly developmental biology, but also genomics, epigenetics, ecology and social science. We contend that evolutionary biology needs revision if it is to benefit fully from these other disciplines. The data supporting our position gets stronger every day.

Yet the mere mention of the EES often evokes an emotional, even hostile, reaction among evolutionary biologists. Too often, vital discussions descend into acrimony, with accusations of muddle or misrepresentation. Perhaps haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front to those hostile to science. Some might fear that they will receive less funding and recognition if outsiders -- such as physiologists or developmental biologists -- flood into their field.

Thursday, October 9, 2014

And I say to the grownups, if you want to deny evolution and live in your world that's completely inconsistent with everything we observe in the universe, that's fine. But don't make your kids do it because we need them. We need scientifically literate voters and taxpayers for the future. We need engineers that can build stuff, solve problems.

Monday, October 6, 2014

Olson essentially took off the gloves in response to an “attack” that was “launched” by Discovery Institute. Olson’s use of one interviewee’s positive response about this seems as selective as his choice of “Icons” (i.e. Haeckel’s embryos) and his choice of interviewees with which to debate evolutionary “truths.” Having talked personally (not an interview) with John Calvert, I can say you will not hear such a glowing review about fair representation. Calvert says that Olson edited his interview with Calvert to tell a very different story about the search for Haeckel’s embryos than what actually took place. In Flock there is a time lapse with Olson’s narration filling in the gap implying that Calvert was searching for the most recent textbook using Haeckel’s embryos and could only find it in a very old textbook, though Calvert intimates that it was a convenient source to show the pictures. Upon watching Flock I was sure that I had seen Haeckel’s embryos twice (two different books by evo-devo biologists) just that month, but even in relatively short books I had a hard time finding the exact locations of the pictures, even while consulting the indices. Illustrations recently viewed were hard to find even when I knew exactly which books to look in. Calvert thinks Olson was both unfair and disingenuous.

Of course, the obvious question would be to next ask: “So just to clarify, you are saying that there are people around that remember George Washington?” You have to wonder why Olson doesn’t ask for clarity on that point.

Is Jonathan Wells in fact a "biologist"? Science Citation Index cites two abstracts (1995) which he coauthored. Ironically one is Molecular Biology of the Cell 6, 666. Clearly he's not currently an active research biologist. His educational goals were apologetic, not scientific. He's a minister in the Unification Church (a "Moonie" in popular culture, see home page). His goal in obtaining a biology Ph. D. was to discredit Darwinism rather than to understand biology. This is hardly scientific objectivity.

More motive-mongering. Wells can’t be a biologist because he has the wrong motives. I wonder how many of the 94% of bio PhDs who are atheists and/or agnostics consider “understanding biology” and “discrediting” intelligent design to not only be non-conflicting, but to be nearly synonymous. How many consider “understanding biology” and “discrediting” theism to not only be non-conflicting but mutually reinforcing? How many actively tell their students this? They are a dime a dozen. “Moonie” is not quite so neutral a term as “Mormon”— I doubt that any Unification follower would generally accept “Moonie”. In their heyday, the Moonies were seen as yet another weird thing in the cultural upheaval of the 70s, and the heirs of positivism take delight in associating Wells with that epithet. Wells can’t be a scientist: he’s a religious minister after all, and in one of them weird cults to boot.

Sunday, September 28, 2014

Accompanying the funny cartoon below was an explanation by a blogger about why chimps are super-smart and we humans shouldn't think too highly of ourselves. The cartoon itself seems aimed at reducing all human exceptionalism to a primate urge. (I think the urge for academics to outpublish each other is more easily traced to that urge.) It makes better humor than philosophy.

Basically chimps are pretty good problem-solvers (and so are octopi for that matter) and they more or less form a sort of strategy or cognitive map of a situation to deal with or navigate a particular problem. What the psychologists are calling metacognition in this case is recognition of underdetermination or sense of (a lack of) certainty. In fact, any ability to revise that map of the problem space is in some sense metacognition.

Of course, many animals have brains that recognize all sorts of things: faces, predators, disorder, direction of motion, spatial relationships. An animal that finds a better vantage point when the view is unclear is doing something analogous; investigating when the cognitive map is hazy is a similar instinct for any problem-solver like a raven or an ape. Can there be much effective problem-solving there without some recognition of underdetermination, without some sense of uncertainty bordering on confusion? It seems like lumping that in with the way humans think about their thinking is extrapolation-turned-polysemy. It stretches credulity.

But the fact that a chimp can recognize when the cognitive map is shaky-- it seriously raises the question of whether a chimp has what it takes to do evolutionary science. ;-)

Saturday, September 27, 2014

I didn't plan the title of my post... It leapt from my fingers as I started typing and the title of the famous science fiction short story somehow seemed appropriate.

I came across a post from Jerry Coyne, anticreationist extraordinaire, which exemplifies for me and reminds me just how bankrupt the materialist, secularist view of humanity really is.

When a male lion invades another group and kills the cubs, when a chimp tears another chimp to bits, those are just bits of nature, and aren’t seen as wrong. And the amorality of nature is touted even by those who realize that our primate relatives show rudiments of morality, . . . . is it really true that all of nature, including primate societies, must be seen as amoral, while human actions must be judged by this thing called “morality”?

Yet, it surprises me to find that recapitulation precedes both Darwin and Haeckel, and that structuralism seems to have had a rich pre-Darwin history.

Serres had been influenced by the theoretical developments in German biology, most notably by early versions of the recapitulation theory proposed by Carl Friedrich Kielmeyer in 1793 and Johann Friedrich Meckel’s theory of arrests of development in 1811. Like Meckel, Serres believed that it was necessary to study the transitional forms of embryos to understand the permanent adult forms of vertebrates. Doing so, he assumed, would reveal that the developed forms of the lower classes of animals – invertebrates, for example –mimicked the intermediate embryonic forms of higher vertebrates. This idea of development was expressed in the Meckel-Serres Law, and distinguished from the later evolutionary accounts of the recapitulation theory proposed by Ernst Haeckel. Serres’ idea of arrests of development, and Geoffroy’s understanding of it, was transcendental rather than evolutionary. For transcendental anatomists like Serres and Geoffroy, the semblances discovered in embryonic stages reflected a particular metaphysical view of life and a philosophy of anatomy exemplified by Geoffroy’s principle of the unity of composition. The similarities inferred by these kinds of embryological studies did not necessarily represent the similarities of structure between vertebrates and invertebrates as an actual empirical fact of transformation from one species to another (i.e. an evolutionary account), but rather they represented the abstraction of an ideal type required by anatomists to form general laws of development and morphology in biology (i.e. a transcendental account). In other words, the principle of unity, the theory of analogies, the theory of arrests of development and the search for homologies were all regulative principles that served as conditions for the possibility of scientific discoveries in the field of anatomy.

- See more at: http://embryo.asu.edu/pages/essay-cuvier-geoffroy-debate#sthash.RsjBneyG.dpuf

Tuesday, September 23, 2014

Virtually all of the non-creationist opposition to the modern theory of evolution, and all of the minimal approbation of [Coyne's University of Chicago colleague James] Shapiro's views, come from molecular biologists. I'm not sure whether there's something about that discipline (the complexity of molecular mechanisms?) that makes people doubt the efficacy of natural selection, or whether it's simply that many molecular biologists don't get a good grounding in evolutionary biology.

LOL (I thought I heard for the last 15 years that evolutionary theory was molecular biology...)

Sunday, September 21, 2014

First I'll talk about the peer-reviewed literature that Randy Olson brings up, and then I'll bring up some peer-reviewed literature that contradicts him.

In Randy Olson's "Pulled Punches" extra for his Flock of Dodos, Olson references an article in The Quarterly Review of Biology ... and mentions the "peer-reviewed" status of said journal to bolster his claims about Haeckel's embryos. As I've expressed elsewhere, I find Olson's choice of this particular example (which he says he picked for personal reasons--presumably because he thought himself particularly knowledgeable on the subject) of that particular book (Icons of Evolution) to represent Intelligent Design to be a loaded choice.

The authors of Olson's touted article have been key figures in the neo-Darwinian public policy think tank NCSE (National Center for Science Education) which is dedicated to having neo-Darwinian theories and hypotheses taught uncritically, and to discrediting Intelligent Design by conflating it with creationism and by promoting ad hominem arguments, and which played a key role in the mistreatment of Richard Sternberg at the Smithsonian. Kevin Padian in particular dislikes Wells' criticism of his dino-bird theories, even though Wells' criticism is probably tame compared to that of paleornithologist Dr. Alan Feduccia.

At any rate, Padian and Gishlik's article seems to claim that Wells did not publish research-based papers after getting his PhD nor did engage in any research, a claim contradicted by Carolyn Larabell. The appearance of this spewing of "pro-science" blatherskite in Quarterly Review says more about the journal than it does about the article. No amount of peer review can make a journal avoid libel, it seems. Nor apologize for it. The fact that Quarterly Review has become a haven for this level of attack on Jonathan Wells, an attack all the more cheapened by associating Dr. Wells with a fictional murderous con artist (in the title no less), demeans its status as a scholarly journal. Why haven't we heard about the Talented Mr. Richards and the Talented Mr. Gould?

It was not long after that creationists and advocates of intelligent design ignited thousands of websites in an electronic auto-de-fé wherein Haeckel's reputation and that of Darwinian theory were generally sacrificed to appease an angry God...

Contrary to the evolutionary hourglass model, variations in the adult body plan are often foreshadowed by modifications of early development. ... These modifications of embryonic development are difficult to reconcile with the idea that most or all vertebrate clades pass through an embryonic stage that is highly resistant to evolutionary change. This idea is implicit in Haeckel's drawings...

Saturday, September 20, 2014

Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenetic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data havefailed to reproduce this classical view.[emphases mine]

The abstract continues to save the day: "Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny." In other words, reconciled tree analysis picks the tree that contains the fewest departures/epicycles from the phylogenetic picture from morphology and paleontology.

Friday, September 19, 2014

In his "Punches Pulled" extra for his film Flock of Dodos, Randy Olson goes through a list of things that he left out of the film supposedly to be nice (i.e. to appear less hostile) rather than to keep his film from becoming a schlockumentary.

I direct your attention to his coup-de-gras. He admits that he talked so long to Dr. Michael Behe that he felt tired afterward. Tired? Was there a debate that didn't make it into the film? (He stresses in the film that two other interviewees he didn't debate about evolution because they didn't have the background. Maybe he engaged Michael Behe about his then-forthcoming book Edge of Evolution, a book that discussed the powers of mutation and selection in detail; Flock implies that Behe wasn't doing anything in 2006 other than glorying in the publishing success of Darwin's Black Box.)

In fact, there is almost nothing from his very long talk with Dr. Behe other than the Mt. Rushmore analogy. Briefly the film dwells on the mousetrap analogy--something more central, but is completely weak on it; if the film had got some of Behe's responses to Ken Miller's criticisms, there might have been some substance to the segment. But it's "Mt. Rushmore" that you hear from the lips of Behe. There's a lot more to ID concepts than a Mt. Rushmore analogy, but it seems to be on the basis of that analogy that Olson anticlimactically dismisses ID at the end of the film. Did they talk about Mt. Rushmore and mousetraps for hours, or did they get into mutation frequencies and malaria? What tired out poor Randy?

But I digress. This coup-de-gras that Olson so graciously left out of his film is that Michael Behe doesn't care. That's right, folks, he doesn't give a scat, and Olson has the goods. More specifically, at the end of what was for Olson a long, grueling interview (Behe appears as relaxed as he did at the beginning of the interview), Olson baits Behe on the politics with which Flock is so deeply concerned. On how the politics affects him, Behe responds that he doesn't have a personal stake in what gets taught to kids in public school because, like so many teachers (here and here), he doesn't send his kids to public school. Perhaps, as a devout Catholic, he would never consider that option anyway. We don't know what followed that sound bite--perhaps a fuller explanation of his "yes and no" answer--nor do we have any idea what was so darn tiring about sitting around outdoors having a relaxed conversation.

Thursday, September 18, 2014

The concept of p-value might just be the most central idea to the notion of counterflow, design, etc.

This is the Fisherian idea that I was taught in biology class at university, and the idea that Dembski has argued is more fundamental to theory choice than the likelihood inference that Elliot Sober promotes.

So earlier this week I was thinking about von Baerian development and considering a specifically non-recapitulatory view of The Vertebrate Embryo and was thinking, "Could the majority of fish be considered more specialized in terms of the general vertebrate pattern, with the more amphibian-like fish being the archetype rather than the specialization.

Lo and behold, I came across something in Stuart Kauffman's work that evidence seems to have been mounting that the swim bladder came from the lung, not the other way around! It would be even more intriguing if the archetype for fish were something even more like an amphibian, say a sarcopterygian like Tiktaalik, rather than the more numerous actinopterygians. The actinopterygians depict for us how (bony) fish are different from other vertebrates.

Now, is it possible that we could learn things about vertebrate development thinking this way much more efficiently than we could with this quasi-Haeckelian recapitulatory progressivism?

The story as I knew it was that fish somehow developed a swim bladder around the time they replaced cartilage with bone. Since utility is the mother and father of invention in the Darwinian world, the usefulness of swim bladders for pelagic swimming was sufficient to explain their existence.
If it turns out that lungs were adaptation preceding tetrapods by ages, well then that too is just what one expects in Darwinland.

. . . in 2009, just three years ago . . . the purported fact that 95 percent of the human genome "might as well not be there" was an embarrassment "for creationists," whom in typical Darwinian fashion Dawkins conveniently conflates with intelligent-design advocates. Junk DNA is just what a Darwinist would expect, in other words. Cut to 2012, and now the evident fact that "junk DNA" isn't junk at all but is instead vital for life has become "exactly what a Darwinist would hope for," namely, "to find usefulness in the living world." That is, heads you lose, tails I win. . . . suspiciously convenient self-contradiction. Ah well, as we knew already, being a Darwinist means never having to say "I was wrong."

But it's not a self-contradiction. With Evolution-Did-It , whatever direction the evidence points is just what Dr. Pangloss would expect, because evolution as a theoretical framework can accommodate almost anything.

Even if the upward trends of progressive (teleological) evolution makes more sense for the historical framework that the evolutionary research program has pursued, what value might there be in more devolutionary hypotheses being assumed. (Devolution is not nearly as satisfying and validating to Darwinism as complexity-building evolution.) The alligator is a reptile that is considered the pinnacle of reptilian evolution nor a transition animal but a sort of devolved representative of warm-blooded archosaurs. Ceolocanths are believed to be derived from sarcopterygians. The TTSS1 pump might be better thought of as having devolved from the flagellum. The mimivirus might best thought of as having devolved from a cellular creature. Maybe Tiktaalik, like the alligator is a throwback, an amphibian that thinks its a fish. Cynodonts might be better understood as a devolution from monotremes.

The evolutionary relationships of the fossil [for the eutriconodont mammal Yanoconodon] suggest that either the "modern" middle ear evolved twice, independently or that it evolved and was then lost [i.e devolution]in at least one ancient lineage.

Or maybe some are mosaics because phylic boundaries, as we know them, are a trend, not a rule (otherwise, how would either mosaics or missing links be possible?). Now, Archaeopteryx is no longer the missing link it pretended to be in our textbooks. It is, for now, more like the coelocanth or alligator. It is a mosaic that represents the diversity of archosaurs (though not as radically as ceratopsids which had apparently "recapitulated" and rediscovered their four-footed roots. And if quadruped representatives of the archosaurs were there all along, like the elusive coelocanths, they simply flew under the paleontological radar and avoided the fossil record as many group likely have.

The approach I am taking to this problem is a variant of structural realism, by which I mean that biological phenomena are manifestations of logico-mathematical structures. This perspective is orthogonal to the origins debate, if you will, because all historical actualities are understood to be space-time instances of pre-existing non-temporal possibilities. Within this context one can accept all that is empirically valid in evolutionary biology, while not axiomatically dismissing the position that structures as well as their “real” instantiations have an intelligent cause.

Wednesday, September 17, 2014

Start with part 8 where Baez gets into the relationship to evolution. Some reminder about thermodynamic models:

Physicists love to think about systems that take only a little information to describe. So when they get a system that takes a lot of information to describe, they use a trick called 'statistical mechanics', where you try to ignore most of this information and focus on a few especially important variables. For example, if you hand a physicist a box of gas, they'll try to avoid thinking about the state of each atom, and instead focus on a few macroscopic quantities like the volume and total energy. Ironically, the mathematical concept of information arose first here—although they didn't call it information back then; they called it 'entropy'. The entropy of a box of gas is precisely the amount of information you've decided to forget when you play this trick of focusing on the macroscopic variables. Amazingly, remembering just this—the sheer amount of information you've forgotten—can be extremely useful... at least for the systems physicists like best.

He goes on to say that in biology, there is a lot less information in the system that can be forgotten... This goes back somewhat to the use of "entropy" to correlate to different kinds of information. The (average) loss of uncertainty/entropy in Shannon information, for example. He goes on to talk about alleles as rival hypotheses.

The analogy is mathematically precise, and fascinating. In rough terms, it says that the process of natural selection resembles the process of Bayesian inference. A population of organisms can be thought of as having various 'hypotheses' about how to survive—each hypothesis corresponding to a different allele. (Roughly, an allele is one of several alternative versions of a gene.) In each successive generation, the process of natural selection modifies the proportion of organisms having each hypothesis, according to Bayes' rule!

It appears that this approach looks at information in terms of a distance from a destination state of stability. So in that sense, it is more about relative information.

But what does all this have to do with information? . . . first discovered by Ethan Atkin. Suppose evolution as described by the replicator equation brings the whole list of probabilities pi — let's call this list p —closer and closer to some stable equilibrium, say q. Then if a couple of technical conditions hold, the entropy of q relative to p keeps decreasing, and approaches zero. Remember what I told you about relative entropy. In Bayesian inference, the entropy q relative to p is how much information we gain if we start with p as our prior and then do an experiment that pushes us to the posterior q. So, in simple rough terms: as it approaches a stable equilibrium, the amount of information a species has left to learn keeps dropping, and goes to zero! . . . You can find [precise details] in Section 3.5, which is called "Kullback-Leibler Divergence is a Lyapunov function for the Replicator Dynamic". . . . 'Kullback-Leibler divergence' is just another term for relative entropy. 'Lyapunov function' means that it keeps dropping and goes to zero. And the 'replicator dynamic' is the replicator equation I described above. . . . [This approach] uses information geometry to make precise the sense in which evolution is a process of acquiring information.

But when we’ve got lots of observables, there’s something better than the variance of each one. There’s the covariance matrix of the whole lot of them! Each observable fluctuates around its mean value … but these fluctuations are not independent! They’re correlated, and the covariance matrix says how.All this is very visual, at least for me. If you imagine the fluctuations as forming a blurry patch near the point , this patch will be ellipsoidal in shape, at least when all our random fluctuations are Gaussian. And then the shape of this ellipsoid is precisely captured by the covariance matrix! In particular, the eigenvectors of the covariance matrix will point along the principal axes of this ellipsoid, and the eigenvalues will say how stretched out the ellipsoid is in each direction!

As I recall, the eigenvalues will be in bits of error in terms of the units of the parameters.

Tuesday, September 16, 2014

One of the motivations for the sequence-space probability dispersion matrix is that as a model it might estimate the computational depth of nucleotide sequences, or the relative depth between two nucleotide sequences. How deep is a given nucleotide sequence?

Kauffman writes in a recent foreword that the universe has produced every kind of atom it could produce (an ergodic process, whereas enumerating the realizable proteins is a non-ergodic process), but Leonard Adleman has elsewhere written in "The Rarest Things in the Universe" (among "entropy and information" here) that atoms with higher counts of protons than we've thus far encountered could be considered to have larger depth (and thus be somewhat analogous to Kauffman's sequences).

I am not a physicist, but I suppose it is possible to theorize about an atomic nucleus with a million protons. But what if I want to create one? It appears that producing transuranic elements takes huge amounts of time/energy and the greater the number of protons, the more time/energy it takes. It is even conceivable (to me at least) that there is not enough time/energy available (at least on earth) to actually produce one. Like the prime factorization of , it may exist in theory but not in reality. On the other hand, physicists from Russia and America, using lots of time/energy, have created an atomic nucleus with 118 protons called Ununoctium. Ununoctium is analogous to Childers’ prime factorization; both exist in reality; both were very costly to create.

In his 1979 paper "Time, Space, and Randomness," Adleman develops an idea about "K-potency" motivated by an analogy with thermodynamics, specifically chemical reactions that take much less time going in one direction than the other.

This approach to "one-way functions" is important to crytography, incidentally. His definition for K-potency follows here:

Monday, September 15, 2014

Oh sure natural selection's been demonstrated . . . the interesting point, however, is that it has rarely if ever been demonstrated to have anything to do with evolution in the sense of long-term changes in populations. . . . Summing up we can see that the import of the Darwinian theory of evolution is just unexplainable caprice from top to bottom. What evolves is just what happened to happen.
- Stanley Salthe

[There are] hundreds of other evolutionary scientists (non-creationists) who contend that natural selection is politics, not science, and that we are in a quagmire because of staggering commercial investment in a Darwinian industry built on an inadequate theory.
- Suzan Mazur

Saturday, September 13, 2014

Randy Olson, in his documentary Flock of Dodos that purports to be an objective inquiry into Intelligent Design both as a (possibly) scientific enterprise and as a social phenomenon, talks about a subject interviewed at an ID convention who claimed to be a Darwinist but later seems to have not been.

This subject seemed noteworthy, Olson seems to present, because it seemed unusual to have a non-creationist spouting a teach-the-controversy view, let alone attending an ID conference as something other than a heckler or guerrilla documentarian. Olson's big reveal is that this Darwinist is John Angus Campbell who is (or was) a Fellow at the Discovery Institute. Olson is vague on this point and seems to rely on the audience to assume that Campbell's warm relationship with ID is in conflict with his conception of Darwinism.

Olson elsewhere does include footage of Michael Behe saying he believes in common descent and macro-evolutionary speciation events, and Olson presents Behe as the spokesman for ID in vague terms ("some say" he is the leading expert on Intelligent Design), so it would seem that Behe embraces some form of Darwinism being more or less convinced of several important tenets. Behe is certainly not Darwinist enough for Olson, since he not only denies the sufficiency of natural selection for certain macroevolutionary feats but he also thinks that the influence of an intelligent agent is better explanation that the other rivals of the selectionist point of view. (Olson's film implies that Behe is the leading idea-man of what he obviously considers an anti-evolution movement.)

Thursday, September 11, 2014

The nexus of Pro-Darwin lobby (teachers, pundits, parents, etc.) and biology practitioners worried about the political status of evolutionary science often work together to make this worse, and not simply by hateful negative attacks on their opposition or by failure to dumb it down sufficiently. (A point not made well by Flock of Dodos.)

As with many evolution-related issues, there is at best a double-message going out there. One is that neo-Darwinism has never had any serious deficiencies and therefore never needed any balance or controversy taught, which has been a useful tactic of the NCSE for years. (Whether this is a vestigial behavior--the "pro-science" lobby has evolved much more slowly than the "anti-science" crowd--or whether this is the inherent defensiveness of a dominant paradigm is a story for another time.) The other message is that there is vigorous, healthy debate over what the processes and mechanisms of evolution are, but that since almost all of these are believers in both methodological naturalism and the power of known forces to explain everything, the commonly taught evolutionary hypotheses are unassailable facts (or should be taught as such at any rate).

The former message has certainly hurt Darwinism. How much criticism has there really been against Richard Dawkins by the "pro-science" coalition for his extreme neo-Darwinistic reductionism? Randy Olson's poker-players don't seem bothered by him. The closest that Olson gets at all to noting any challenge to neo-Darwinism (or that there is any diversity in the academic ecosystem) is lumping "process structuralism" in with ID at some point (the "teach the controversy" segment, I think). The fact that Olson can implicitly charge ID as a God-Did-It approach (as his editing choices convey) but not recognize the extent to which much of evolutionary literature has boiled down to Selection-Did-It or Evolution-Did-It says much. In fact, the ideas about how it happened and the mechanisms involved are so complicated at this point, that overconfidence concerning natural selection through most of the 20th century (and continuing now) seems both naive and quaint. I was taught in college that microevolution = macroevolution, essentially, as a fact. As Stuart Newman has pointed out, this overconfidence, while achieving political mileage in jurisprudence, has hurt public perception of evolutionary teaching in general.

Meanwhile Michael Ruse has attacked creationism (no doubt including ID in it) of being more selection-obsessed than the evolution crowd, without (until perhaps lately) giving any credit to this sociological effect. If people tend to conflate anti-Darwinism with anti-evolution, maybe it's because too often the "pro-science" crusaders have conflated Darwinism with evolution.

The second message potentially hurts the general prospect of evolution partly because of this (wait, what do you mean it isn't as simple as natural selection and microevolution?), but also because Selection-Did-It is more obviously replaced by Evolution-Did-It. Evolution has become the Dark Energy of the 21st century. No one agrees what Dark Energy is or how it figures into physics, but Something is causing the galaxies to diverge over time; new species with novel structure and organs have appeared over time and therefore Evolution is the name given to that Power at work. The entire scientific community starts to a resemble a jury that have very conflicting ideas about how the defendant committed the crime and where he committed it, based on contradictory evidences and contradictory interpretations, but are (almost) unanimous in their belief that he is most definitely guilty based on the evidence. (Half the jury are okay his religion, half are okay with his race, and only a few don't like his face, so you can't say they are unanimously prejudiced.)

But if we give the name "Evolution" to the basic pattern being investigated--the changes in biological diversity over geologic time on Earth, the explananda rather than the explanans--neither Intelligent Design in general nor Discovery Institute in particular are any opposition to this. The fact that you can be a creationist within the ID framework, as you can be an evolutionist like Michael Behe, or anything in between, is part of the guilt-by-association tactics by "pro-science" Big Darwin. What the "pro-science" lobby find so threatening about the "Big Tent" of ID is that (a) that it is mostly consonant with theism (i.e. "makes it possible to be an intellectually fulfilled theist") rather than dissonant, and (b) the usual tactics against Young Earth Creationism do not begin to address it.

(Again, two messages: (1) Creationists are not to be trusted because they are evolution-denying hayseeds. (2) ID theorists like Michael Behe who largely embrace evolution are still creationists because they don't rule out theories consonant with "supernatural causation." Collectively, these messages amount to double-speak.)

Certainly, you can be a skeptic of neo-Darwinism without doubting Big Evolution. What Suzan Mazur's work has achieved, perhaps more than anything else, is documenting the stifling effect the neo-Darwinian Synthesis has had on biologists and selection skeptics. But calling evolution skeptics "evolution deniers" (a trope that analogizes with Holocaust denial) is partly ugly political tactic and partly "physics envy" (the idea that biology vies with physics for ontological validity, e.g. in elevating the theoretical status of evolution to that of gravity). Many ID theoreticians believe in some version of selection-oriented evolution and common descent, many are skeptics of one or more accepted evolutionary hypotheses, and some do think the whole evolutionary narrative is a mostly unproductive concept.

The crumbling of the neo-Darwinist edifice has hurt Evolution in more than just a PR sense. If science, as the ACLU has asserted through Judge Jones, is what scientists do, then neo-Darwinism is the strongest, most worked out, and most explanatory theoretical framework for evolution. If it is really as weak as it appears to be, it calls for some serious skepticism of the explanans of evolutionary science, if not the explananda.

Perhaps the biggest failing of Randy Olson's Flock is the attempt to only cast Intelligent Design as a sociological phenomenon (driven by philosophical motives) and does not really get close to doing the same with his own camp, despite his belief in his own objectivity. He shows some of this at work, but doesn't make it part of his documentary's explanation. The explanation he gives concerning them is that they are so erudite (he helps make this point by displaying definitions for the big words they use) that they make poor evangelists for his gospel of truth.